초록 ▼

Ⅳ. 연구개발결과
○ 산자수 형질 관련(총산자수, 생존두수 등)과 연관된 다량의 SNPs 발굴
- 1산차 총산자수와 연관되 SNP 발굴 : 43종 [SSC1(9), SSC2(4), SSC3(4), SSC5(1), SSC6(1), SSC7(1), SSC8(4), SSC10(3), SSC15(2), SSC17(2) ,SSC18(2)]
- 1산차 생존두수와 연된된 SNP 발굴 : 251종 [SSC1(5), SSC2(42), SSC3(4), SSC4(3), SSC5(11), SSC6(7), SSC7(5), SSC8(3),

Ⅳ. 연구개발결과
○ 산자수 형질 관련(총산자수, 생존두수 등)과 연관된 다량의 SNPs 발굴
- 1산차 총산자수와 연관되 SNP 발굴 : 43종 [SSC1(9), SSC2(4), SSC3(4), SSC5(1), SSC6(1), SSC7(1), SSC8(4), SSC10(3), SSC15(2), SSC17(2) ,SSC18(2)]
- 1산차 생존두수와 연된된 SNP 발굴 : 251종 [SSC1(5), SSC2(42), SSC3(4), SSC4(3), SSC5(11), SSC6(7), SSC7(5), SSC8(3), SSC9(127), SSC10(3), SSC13(15), SSC15(12), SSC16(6), SSC18(8)]
○ 재래돼지 표준유전체를 완성함: contig N50 31kb, scaffold N50 17.2Mb
○ 재래돼지 표준유전체에서 듀록 참조유전체와 비교하여 총 913개의 CNV를 발굴하였고, 이중에 재래돼지 특이적인 CNV gain 26개와 loss 30개를 발굴함
○ 산자수 관련 형질 정보를 활용한 통계적 선발 방법 비교 및 우수한 선발 방법에 따른 유의한 유전자 발굴

Abstract ▼

One detailed assignment : This study whole-genome association study was performed for reproductive traits in commercial sows using the PorcineSNP60 BeadChip and Bayesian statistical methods. Genotype analysis was performed using the porcine SNP 60 K beadchip. The GWAS was performed using a mixed-eff

One detailed assignment : This study whole-genome association study was performed for reproductive traits in commercial sows using the PorcineSNP60 BeadChip and Bayesian statistical methods. Genotype analysis was performed using the porcine SNP 60 K beadchip. The GWAS was performed using a mixed-effects model and linear regression approach. A genome-wide association study (GWAS) was conducted using an Yorkshire pigs. The traits included total number born (TNB), number born alive (NBA), number of stillborn (SB), number of mummified foetuses at birth (MUM) and gestation length (GL) in each of the first three parities. We report the associations of related genes(e.g. GLYATL1, OR4D11, NOL4 et al) for each reproductive trait in different parities. These results provide evidence of gene effects having temporal impacts on reproductive traits in different parities. These results provide valuable information about the selective breeding for reproductive traits in pigs. Further validation studies on large populations are warranted to improve our understanding of the complex genetic architecture for pig reproductive traits.
One cooperated assignment : The purpose of this study is to make standard genome of korean domestic pig, comparative analysis, discovery & analysis of SNP, INDEL, and CNV in 60 pig resequencing data, transcriptome & epigenome analysis in reproduction related organs in female pig. Finally, we contructed portal sites for pig genome, transcriptome and epigenomes. Using various NGS sequencing data – paired end, mate pair and fosmid end pair, we made first draft genome of korean domestic pig. Genome size is estimated as 2,554,581,065bp by K-mer analysis and it is similar with pig referenced genome (sus scrofa 10.2). Final assembly has contig N50 31kb, scaffold N50 17.2Mb. Most of them are assigned into chromosome (694 scaffolds), except 9,219 small scaffolds (86Mb). We have found 913 CNVs in korean domestic pigs and it has 25 gain and 30 loss korean domestic pig-specific CNVs. Using 60 resequencing data, we have discovered more than 8.9million homozygous and 18.3 million heterozygous SNPs and it covered more than 99% of duroc reference genome. Overall, sequence depth is about 10X coverage. 16~25 of SNPs on each breed are novel and not found in dbSNP. We had performed population genomics analysis such as phylogenomics, principal component analysis, admixture analysis, LD decay, nucleotide diversity (PI), Tajima’D, Hp (pooled heterozygosity), ROD (Reduction of Diversity), and F-stat. During scanning genomes by 100kb-bin, we have defined domesticated area as ROD >= 0.98 and Z(Hp) <= -3. 1% out of whole gene turned out to be considered as affected during domestication. We have discovered 128 korean domesticated pig specific genes. Using Pathway Studio 9, we have done gene-set enrichment, pathway, network analysis. Phylogenetic tree and PCA revealed that they can be separated into three groups (1) wild-boar, (2) korean domestic pigs and (3) duroc, landrace, minipig, yorkshire. Admixture analysis also showed that korean domestic pigs can be divided into two groups depending on provinces they reside on. Duroc showed high rate of homozygosity and larger LD-block sizes compared with other female-breeding pigs. Overall concordance rate with SNP-chip is more than 99% and ratio of homozygous vs. heterozygous is around 0.5 because sequencing depth is medium 10X coverage. We have used Tuxedo protocol for RNA-Seq data and did statistical analysis to discover house-keeping gene and tissue-specific genes (82~964 depending on each tissue) with 131 ovary-specific genes. Finally, all of the korean domestic pig standard genome, resequencing data, SNP/INDEL/CNV, and expression plots for RNA-Seq had been integrated in pig potal genome site, and it will be open for public soon.
Two cooperated assignment : This study considers a problem of genomic selection (GS) for adjacent genetic markers of Yorkshire pigs which are typically correlated. The GS has been widely used to efficiently estimate target variables such as molecular breeding values using markers across the entire genome. Recently, GS has been applied to animals as well as plants, especially to pigs. For efficient selection of variables with specific traits in pig breeding, it is required that any such variable selection retains some properties: i) it produces a simple model by identifying insignificant variables; ii) it improves the accuracy of the prediction of future data; and iii) it is feasible to handle high-dimensional data in which the number of variables is larger than the number of observations. In this study, we applied several variable selection methods including least absolute shrinkage and selection operator (LASSO), fused LASSO and elastic net to data with 47K single nucleotide polymorphisms and litter size for 519 observed sows. Based on experiments, we observed that the fused LASSO outperforms other approaches.

목차 Contents

• 표지 ... 1
• 제출문 ... 2
• 요약문 ... 3
• SUMMARY ... 5
• 목차 ... 7
• 제 1 장 서 론 ... 8
• 제 2 장 국내외 기술개발 현황 ... 12
• 제 1 절 국내 기술개발 현황 ... 12
• 제 2 절 국외 기술개발 현황 ... 13
• 제 3 절 국내외 연구현황 비교 및 필요 연구 분야 ... 17
• 제 3 장 연구개발수행 내용 및 결과 ... 22
• 제 1 절 NGS 기법을 활용한 돼지 유전체 해독 및 산자수 연관 SNP 발굴 ... 22
• 제 2 절 돼지 대용량 유전체와 전사체의 어셈블리 및 생물정보학 해석 ... 29
• 제 3 절 진화 유전체 선발 및 생물정보학적 분석 연구 ... 84
• 제 4 장 연구개발목표 달성도 및 대외기여도 ... 88
• 제 1 절 목표대비 달성도 ... 88
• 제 2 절 정량적 성과(논문게재, 특허출원, 기타) ... 89
• 제 5 장 연구개발결과의 활용계획 ... 90
• 제 6 장 연구개발과정에서 수집한 해외과학기술정보 ... 91
• 제 7 장 기타 중요 변동사항 ... 92
• 제 1 절 연구책임자 변경 ... 92
• 제 8 장 국가과학기술종합정보시스템에 등록한 연구장비 현황 ... 93
• 제 9 장 참고문헌 ... 94
• 끝페이지 ... 96